Many of the centers in Amed and Tulamben do not offer a discount for having your own gear. As said above, the prices are pretty cheap as is and include a guide, which in many parts of the world is an added cost you would incur. Dive centers also pay the tourist fees at the dive sites as well as the porter costs.
If they gave you a 10% discount for having your own gear, you would save a whopping $6.58 on two dives if the cost is IDR 1,000,000 for two, although I know they tend to be the cheapest of all the centers so they might be closer to 850,000 for two.
Having said that, different policies for different locations makes zero sense and should be called out but it does not surprise me one bit.